A variety of technologies exist to treat biomass. Oftentimes, prior to such “treating” of biomass, the biomass is “pretreated” in order to enhance biodigestibility of the biomass during treatment. The biomass pretreatment process can be performed in a reactor at high temperatures and pressures in the presence of a liquid. Certain agents, such as acids, alkalis, and oxidizers are often used to enhance this process. Example pretreatment processes include, but are not limited to, those that are base catalyzed (ammonia, alkaline-peracetic acid, alkaline peroxide, alkaline-solvent, lime, lime under oxygen pressure, sodium hydroxide), non catalyzed (autohydrolysis, hot water, hot water −pH neutral, steam), acid catalyzed (concentrated or dilute acid using sulfuric acid, hydrochloric acid, peracetic acid, phosphoric acid, sulfur dioxide), solvent based (organosolv, other solvents), and chemical based (peroxide, wet oxidation).